None of the listed choices would be my personal choices for respective seasons' best (and I'm surprised it's not Dead Stop or something instead of Carbon Creek as a choice for Season Two), but ...

... I have to go with Twilight here. Shuttlepod One would be runner-up, but I think Twilight has more 'weight' to it. It's more a poignant tragedy. It's more epic. And that doesn't always equal good or better. Shuttlepod One is a great character piece, and I love it. But in this instance ... I just think that Twilight is better. It gave us, as viewers, a better perspective/appreciation of the whole Xindi threat by showing what the consequences of potential failure would be. And it had some of Archer and T'Pol's best interactions. And the ending, where he commented that she would make a good nurse ... was very poignant. Though the characters didn't know that, we did. Just how close they came from having that future be the real future ...

It's the season four episode where Organians (in non-corporeal form, often as Mayweather and Reed) study the response of the Enterprise crew to the infection of Hoshi Sato and Tucker by a fatal silicon-based virus brought on board during an away mission. Archer ends up risking his life to save them and one of the Organians rewards him by saving Tucker, Hoshi and his life.

Good one, but doesn't hold a candle to Twilight, which I think is one of the best of Enterprise.